Web Exercise – Phylogeny for the Faint of Heart

For the quiz this week read the tutorial on phylogenetics by Sandra L. Baldauf published in Trends in Genetics (2003, vol. 19, pp. 345-351, pdf file found here).  Baldauf provides an excellent overview of phylogenetic analysis, the terminology, approaches, resources and overall reasons for using it. In class we will do some of the exercises she mentions, so you will need to master the basic ideas. After reading the article, be prepared to answer the following questions.

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1. Tree-building is basically reconstructing the past using information from the present. Rooted and unrooted trees both represent evolutionary relationships among genes or organisms, but rooted ones provide information about the branching order of the groups or clusters being compared. How is a tree typically rooted?
 
 
 

2. Homologous sequences may be either orthologous or paralogous. How do they differ? Mention how each can convey information about the evolutionary past of a group of organisms.
 
 
 

3. Multiple sequence alignments arrange sequences so that the assumed homologous positions are in columns. How is this done? What rules are followed? 

 
 

4. In phylogenetic analysis, how do distance methods (neighbor-joining, for example) differ in approach from discrete data methods (parsimony, for example)? Which ones are generally faster? Which ones convey the most information about the evolutionary past?
 
 
 

5. In phylogenetic analysis, what is bootstrapping? What is 'long-branch attraction'?